Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate 206911 DVU1466 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >MicrobesOnline__882:206911 Length = 308 Score = 108 bits (269), Expect = 3e-28 Identities = 82/268 (30%), Positives = 132/268 (49%), Gaps = 25/268 (9%) Query: 24 VVKVGGAVLRDDV--DALTSSLSFLQEVGLTPIVLHGAGPQLDEELTAVGIQKKTVNGFR 81 V+K GG ++D+ A +++ L+ VG+ P+++HG GPQ+ + L + IQ G R Sbjct: 30 VIKYGGHAMKDEALKKAFALNVALLKLVGINPVIVHGGGPQIGKMLEQLNIQSHFREGLR 89 Query: 82 VTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITG--GVF------------EAHYL 126 VT TM +V V N +++ + GA+A ++G G+ EA Sbjct: 90 VTDDATMDVVEMVLVGKVNKEIVNQMNLAGAKAVGLSGKDGMLIRARKMEMVISKEAQAP 149 Query: 127 DQETYGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQILNINADVAANELVHVLQP 186 + G VG + VN + + R +PVIA +G +G+ NINAD A + L+ Sbjct: 150 EIIDLGKVGEVMGVNTTLLRSLERDGFVPVIAPVGVDDNGETYNINADAVAGAVAAALKA 209 Query: 187 YKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMKLKIEQIKHLLDRLP--L 244 +++ LT G+LD D K+I S+N+ E L + GGM I ++K L+ L + Sbjct: 210 KRLLLLTDVAGILDHDKKLIRSVNM-REAVNLFSDGTLTGGM---IPKVKCCLEALEEGV 265 Query: 245 ESSVSITRPAD--LAKELFTHKGSGTLI 270 E ++ I + + EL T KG GT I Sbjct: 266 EKAMIIDGRTENCILLELLTDKGVGTEI 293 Lambda K H 0.320 0.136 0.399 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 254 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 421 Length of database: 308 Length adjustment: 29 Effective length of query: 392 Effective length of database: 279 Effective search space: 109368 Effective search space used: 109368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory